This thesis concerns molecules with potential uses for information storage on the atomic scale. Density functional theory (DFT) calculations are used to study the molecules in depth, to further understand their properties and to ascertain whether they are suited to such applications. Throughout this thesis, particular attention is paid to the effect of the surface on the properties of the adsorbates. This includes the effect of dispersion interactions, the quenching effect of a metal surface on the spin moment of the adsorbate and the role of a polarising thin film in stabilising various charge states of a molecule. The molecule 4-carboxy-TEMPO (4CT) is studied, adsorbed on Cu(110). In gas-phase, this molecule has an unpaired electron on the NO group, surrounded by methyl groups which could shield the radical from being quenched when adsorbed on a metal surface. Spin-polarised DFT calculations are used in combination with scanning tunnelling microscopy simulations to identify the adsorption geometry of 4CT on Cu(110). Information about the electronic structure of the system from the DFT calculations is then used to determine that the NO radical is not preserved upon adsorption on Cu(110). Following this, DFT calculations of cobalt tetraphenylporphyrin (CoTPP), also adsorbed on Cu(110), are used to examine the magnetic properties of the system. Specifically, whether the spin moment of the central Co atom is quenched upon adsorption on the metal. The treatment of the highly-correlated d-electrons of the Co atom is problematic for semi-local DFT, such as GGA. As a result, the impact of the inclusion of an on-site Coulomb repulsion, U , is studied to understand its effect on the spin moment of the Co. Methods for the self-consistent calculation of U are assessed and ivcomparisons are made with experimental measurements of the spin moment of the Co by X-ray magnetic circular dichroism (XMCD). An overestimation of the value of U by self-consistent methods is discovered, which leads to qualitatively wrong magnetic behaviour, however, it is found that the experimentally observed moment is observed for calculations carried out for a narrow range of U -values. The copper complex, bis-dibenzoylmethanato-copper (Cu(dbm) 2 ), is next to be studied. Experimental work on this complex showed that, upon being exposed to an STM voltage pulse, it exhibited a reversible switching behaviour when adsorbed on a NaCl bilayer on Cu(111) and Cu(100). By using a recently developed perfect conductor (PC) model, where the metal substrate is replaced by a PC, calculations of the oxidation and reduction of this system can be carried out. Such calculations reveal that the ionic polarisation of the NaCl thin-film is able to stabilise various charge-states of the complex. Furthermore, it is shown that charging of the complex is not sufficient to explain the switching, with a new charged state being found to be necessary to explain the switching process. This new charge state, predicted by the theoretical calculations, was later observed experimentally. Finally, a study of the hydrogen transfer in porphycene (Pc) on Cu(110) is conducted. A nudged elastic band calculation is used to determine the minimum energy path and barrier height of hydrogen transfer in this molecule, showing that the transfer proceeds step-wise through a short lived trans state, and not via concerted motion of the hydrogens. By calculation of the frequencies of the N-H modes of the adsorbed molecule it is shown that the zero point energy of the hydrogens has a significant role in lowering the barrier of the transfer process. These results show the important part played by the surface in the behaviour of the adsorbates, and illustrate how interaction with a surface can qualitatively alter the behaviour of adsorbates in comparison to the gas-phase. Theory and experiment are brought into contact and used to both refine theoretical understanding, and to direct further experimental studies.